==15617== Memcheck, a memory error detector ==15617== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==15617== Using Valgrind-3.26.0 and LibVEX; rerun with -h for copyright info ==15617== Command: /home/runner/work/Chaste/Chaste/Chaste/chaste-build-dir/cell_based/test/TestMutableVertexMeshOperationsWithPopulationSrn -malloc_debug -malloc_dump -memory_info ==15617== Parent PID: 14966 ==15617== ==15617== ==15617== FILE DESCRIPTORS: 11 open (6 inherited) at exit. ==15617== Open file descriptor 10: /dev/shm/open_mpi.0000 ==15617== at 0x131E2536: __open_nocancel (open64_nocancel.c:39) ==15617== by 0x13166BC3: shm_open@@GLIBC_2.34 (shm_open.c:46) ==15617== by 0x1884A89E: opal_shmem_posix_shm_open (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x1884AA71: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18849C38: ??? (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18849F97: opal_shmem_base_select (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18719159: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x107E90E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EE49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EF2C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107E618F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x10820627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0xF7C7446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15617== by 0xEEDA2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15617== by 0xEEDA327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15617== by 0x4022633: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==15617== by 0x401CD01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==15617== by 0x401F9DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==15617== by 0x401F871: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15617== by 0x401FF6B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15617== by 0x401B158: main (TestMutableVertexMeshOperationsWithPopulationSrn.cpp:18) ==15617== { CoreError:FdNotClosed fun:__open_nocancel fun:shm_open@@GLIBC_2.34 fun:opal_shmem_posix_shm_open obj:/usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5 obj:/usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5 fun:opal_shmem_base_select fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==15617== Open file descriptor 9: ==15617== at 0x131F096B: eventfd (syscall-template.S:120) ==15617== by 0x188AA188: evutil_eventfd_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A8395: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A8704: evthread_make_base_notifiable (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A89F1: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x1880F0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x1880F1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18719120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x107E90E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EE49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EF2C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107E618F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x10820627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0xF7C7446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15617== by 0xEEDA2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15617== by 0xEEDA327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15617== by 0x4022633: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==15617== by 0x401CD01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==15617== by 0x401F9DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==15617== by 0x401F871: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15617== by 0x401FF6B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15617== by 0x401B158: main (TestMutableVertexMeshOperationsWithPopulationSrn.cpp:18) ==15617== { CoreError:FdNotClosed fun:eventfd fun:evutil_eventfd_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:evthread_make_base_notifiable fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==15617== Open file descriptor 8: ==15617== at 0x131E12BB: pipe2 (syscall-template.S:120) ==15617== by 0x188A9F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188AC579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188AC774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x1880F0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x1880F1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18719120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x107E90E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EE49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EF2C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107E618F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x10820627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0xF7C7446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15617== by 0xEEDA2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15617== by 0xEEDA327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15617== by 0x4022633: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==15617== by 0x401CD01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==15617== by 0x401F9DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==15617== by 0x401F871: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15617== by 0x401FF6B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15617== by 0x401B158: main (TestMutableVertexMeshOperationsWithPopulationSrn.cpp:18) ==15617== { CoreError:FdNotClosed fun:pipe2 fun:evutil_make_internal_pipe_ fun:evsig_init_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==15617== Open file descriptor 7: ==15617== at 0x131E12BB: pipe2 (syscall-template.S:120) ==15617== by 0x188A9F87: evutil_make_internal_pipe_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188AC579: evsig_init_ (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188AC774: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x1880F0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x1880F1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18719120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x107E90E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EE49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EF2C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107E618F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x10820627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0xF7C7446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15617== by 0xEEDA2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15617== by 0xEEDA327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15617== by 0x4022633: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==15617== by 0x401CD01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==15617== by 0x401F9DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==15617== by 0x401F871: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15617== by 0x401FF6B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15617== by 0x401B158: main (TestMutableVertexMeshOperationsWithPopulationSrn.cpp:18) ==15617== { CoreError:FdNotClosed fun:pipe2 fun:evutil_make_internal_pipe_ fun:evsig_init_ obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==15617== Open file descriptor 4: ==15617== at 0x131F146B: epoll_create1 (syscall-template.S:120) ==15617== by 0x188AC6FA: ??? (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x188A88AA: event_base_new_with_config (in /usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1) ==15617== by 0x1880F0D7: opal_event_base_create (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x1880F1E8: opal_event_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x18719120: opal_init (in /usr/lib/x86_64-linux-gnu/libopen-pal.so.80.0.5) ==15617== by 0x107E90E7: ompi_rte_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EE49F: ??? (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107EF2C3: ompi_mpi_instance_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x107E618F: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0x10820627: PMPI_Init_thread (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7) ==15617== by 0xF7C7446: PetscInitialize (in /usr/lib/x86_64-linux-gnu/libpetsc_real.so.3.24.4) ==15617== by 0xEEDA2D9: PetscSetupUtils::InitialisePetsc() (PetscSetupUtils.cpp:80) ==15617== by 0xEEDA327: PetscSetupUtils::CommonSetup() (PetscSetupUtils.cpp:88) ==15617== by 0x4022633: PetscSetup::setUpWorld() (FakePetscSetup.hpp:70) ==15617== by 0x401CD01: CxxTest::RealWorldDescription::setUp() (RealDescriptions.cpp:266) ==15617== by 0x401F9DE: CxxTest::TestRunner::runWorld() (TestRunner.h:43) ==15617== by 0x401F871: CxxTest::TestRunner::runAllTests(CxxTest::TestListener&) (TestRunner.h:23) ==15617== by 0x401FF6B: CxxTest::ErrorFormatter::run() (ErrorFormatter.h:47) ==15617== by 0x401B158: main (TestMutableVertexMeshOperationsWithPopulationSrn.cpp:18) ==15617== { CoreError:FdNotClosed fun:epoll_create1 obj:/usr/lib/x86_64-linux-gnu/libevent_core-2.1.so.7.0.1 fun:event_base_new_with_config fun:opal_event_base_create fun:opal_event_init fun:opal_init fun:ompi_rte_init obj:/usr/lib/x86_64-linux-gnu/libmpi.so.40.40.7 fun:ompi_mpi_instance_init fun:ompi_mpi_init fun:PMPI_Init_thread fun:PetscInitialize fun:_ZN15PetscSetupUtils15InitialisePetscEv fun:_ZN15PetscSetupUtils11CommonSetupEv fun:_ZN10PetscSetup10setUpWorldEv fun:_ZN7CxxTest20RealWorldDescription5setUpEv fun:_ZN7CxxTest10TestRunner8runWorldEv fun:_ZN7CxxTest10TestRunner11runAllTestsERNS_12TestListenerE fun:_ZN7CxxTest14ErrorFormatter3runEv fun:main } ==15617== ==15617== HEAP SUMMARY: ==15617== in use at exit: 126,484 bytes in 902 blocks ==15617== total heap usage: 40,836 allocs, 39,934 frees, 11,298,387 bytes allocated ==15617== ==15617== LEAK SUMMARY: ==15617== definitely lost: 0 bytes in 0 blocks ==15617== indirectly lost: 0 bytes in 0 blocks ==15617== possibly lost: 0 bytes in 0 blocks ==15617== still reachable: 11,981 bytes in 45 blocks ==15617== suppressed: 114,503 bytes in 857 blocks ==15617== Reachable blocks (those to which a pointer was found) are not shown. ==15617== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==15617== ==15617== For lists of detected and suppressed errors, rerun with: -s ==15617== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 33 from 33)